package compbio.ws.client;

import compbio.metadata.AllTestSuit;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.fail;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.Writer;
import java.io.OutputStreamWriter;
import java.net.ConnectException;
import java.util.ArrayList;
import java.util.List;

import javax.xml.ws.WebServiceException;

import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;

import compbio.data.msa.FoldWS;
import compbio.data.msa.JABAService;
import compbio.data.msa.SequenceAnnotation;
import compbio.data.sequence.Alignment;
import compbio.data.sequence.ClustalAlignmentUtil;
import compbio.data.sequence.ConservationMethod;
import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.ScoreManager;
import compbio.data.sequence.SequenceUtil;
import compbio.data.sequence.UnknownFileFormatException;
import compbio.metadata.AllTestSuit;
import compbio.metadata.JobSubmissionException;
import compbio.metadata.LimitExceededException;
import compbio.metadata.Option;
import compbio.metadata.PresetManager;
import compbio.metadata.ResultNotAvailableException;
import compbio.metadata.RunnerConfig;
import compbio.metadata.UnsupportedRuntimeException;
import compbio.metadata.WrongParameterException;
import compbio.runner.conservation.AACon;
import compbio.util.SysPrefs;
import compbio.ws.server.RNAalifoldWS;


public class TestRNAalifoldWS {
	
	SequenceAnnotation<RNAalifoldWS> foldws;
	
	@BeforeTest(groups = {AllTestSuit.test_group_webservices})
	void initConnection() {
		
		try {
			JABAService client = Jws2Client.connect(
					"http://localhost:8080/jabaws", Services.RNAalifoldWS);
			foldws = (SequenceAnnotation<RNAalifoldWS>) client;
		} catch (ConnectException e) {
			e.printStackTrace();
			fail(e.getMessage());
		} catch (WebServiceException e) {
			e.printStackTrace();
			fail(e.getMessage());
		}
	}

	
	@Test(groups = {AllTestSuit.test_group_webservices})
	public void testFold() throws FileNotFoundException, IOException,
			UnknownFileFormatException {
		
//		String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
//				+ File.separator;
		
		Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(
				AllTestSuit.test_input_aln));
		
		List<FastaSequence> fsl = aln.getSequences();
		
		try {
			List<Option<RNAalifoldWS>> options  = new ArrayList<Option<RNAalifoldWS>>();
			options.add(foldws.getRunnerOptions().getArgumentByOptionName("--mis"));
			options.add(foldws.getRunnerOptions().getArgumentByOptionName("-p"));
			options.add(foldws.getRunnerOptions().getArgumentByOptionName("--MEA"));
			
			System.out.println("TestRNAalifoldWS: print options: " + options.toString());
			
			String jobId = foldws.customAnalize(fsl, options);
			System.out.println("J: " + jobId);
			ScoreManager result = foldws.getAnnotation(jobId);
			System.out.println("fold results: \n" + result.toString());
			
			Writer writer = new OutputStreamWriter(System.out);
			result.writeOut(writer);
			
			assertNotNull(result);
			
		} catch (UnsupportedRuntimeException e) {
			e.printStackTrace();
			fail(e.getMessage());
		} catch (LimitExceededException e) {
			e.printStackTrace();
			fail(e.getMessage());
		} catch (JobSubmissionException e) {
			e.printStackTrace();
			fail(e.getMessage());
		} catch (ResultNotAvailableException e) {
			e.printStackTrace();
			fail(e.getMessage());
		} catch (WrongParameterException e) {
			e.printStackTrace();
			fail(e.getMessage());
		}
	}
}